Markers + reference

Discostella

3 species · Stephanodiscaceae · Stephanodiscales

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Species 3
Genome length 128–129 kb
Candidate markers 355
Primer pairs 85

Genome-wide nucleotide diversity

Sliding-window nucleotide diversity
Sliding-window nucleotide diversity (π) across the plastome.

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 355 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
petA-chlI Genome 675 0.2997 0.94 84.1 yes View details
ftsH-trnT-UGU Genome 257 0.1924 0.98 74.6 yes View details
trnP-UGG-ycf89 Genome 706 0.2315 0.76 77.7 yes View details
ycf89-rns Genome 491 0.2279 0.95 79.7 yes View details
thiS-psb28 Genome 288 0.2604 1.00 77.0 yes View details
rns-ycf89 Genome 491 0.2258 0.95 79.6 yes View details
ycf89-trnP-UGG Genome 706 0.2315 0.76 77.7 yes View details
psbX-rbcS Genome 422 0.2107 0.98 81.3 yes View details
rpl6 Genome 540 0.0765 1.00 81.3 yes View details
rpoB-rps20 Genome 399 0.2065 0.97 80.0 yes View details
ccsA Genome 978 0.0723 1.00 80.0 yes View details
ccsA Genome 978 0.0723 1.00 80.0 yes View details
trnS-GCU-trnD-GUC Genome 71 0.1737 1.00 79.8 yes View details
trnQ-UUG-trnR-ACG Genome 64 0.1333 0.86 79.7 yes View details
rpl1-rpl12 Genome 80 0.1417 1.00 79.4 yes View details
trnD-GUC-petN Genome 194 0.1719 0.98 79.4 yes View details
psaJ-trnP-UGG Genome 136 0.1679 0.99 79.4 yes View details
Candidate markers include all hotspot labels marked in the diversity plot, listed in genomic order, plus the top 10 remaining regions by MarkerSeek score. Primer design is attempted for every listed region. Primer available: yes means at least one valid primer pair was found; no means no valid pair passed screening; NA means primer design was skipped.

Primer pairs

Showing the top 30 of 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbX-rbcS_p1 psbX-rbcS GCGATAAAATTTGCTAATGAAGTTGT CCCTGAAGGTAGCCGTTATT 408–476 1.000 52.0
psbX-rbcS_p2 psbX-rbcS GCGATAAAATTTGCTAATGAAGTTGT CAGTGTTCAAGCTAACCCTGA 423–491 1.000 52.0
psbX-rbcS_p3 psbX-rbcS GCGATAAAATTTGCTAATGAAGTTGT TGTTCAAGCTAACCCTGAAGG 420–488 1.000 52.0
psbX-rbcS_p4 psbX-rbcS GCGATAAAATTTGCTAATGAAGTTGT ACAGTGTTCAAGCTAACCCTG 424–492 1.000 52.0
psbX-rbcS_p5 psbX-rbcS GCGATAAAATTTGCTAATGAAGTTGT ACAGTGTTCAAGCTAACCCT 424–492 1.000 52.0
rpl1-rpl12_p1 rpl1-rpl12 TGCGAAAATTATCCCGACGT GCCATCATAATACCCCCACC 903–909 0.667 71.7
rpl1-rpl12_p2 rpl1-rpl12 TGCGAAAATTATCCCGACGT AACGACGATGCTGTACGATC 1359 0.333 51.8
rpl1-rpl12_p3 rpl1-rpl12 TGCGAAAATTATCCCGACGT CGACGATGCTGTACGATCAA 1357 0.333 51.8
rpl1-rpl12_p4 rpl1-rpl12 TGCGAAAATTATCCCGACGT GGCCATCATAATACCCCCAC 910 0.333 51.5
rpl1-rpl12_p5 rpl1-rpl12 CAATTGCGTACAACGGTGAC AACGACGATGCTGTACGATC 1189 0.333 51.5
rpoB-rps20_p1 rpoB-rps20 ATAAGCGGCTCTCAGTAGGT CGTTGCGGATTATTTCGACG 1542 0.333 52.6
rpoB-rps20_p2 rpoB-rps20 AAGCGGCTCTCAGTAGGTAA CGTTGCGGATTATTTCGACG 1540 0.333 52.0
rpoB-rps20_p3 rpoB-rps20 AGCGGCTCTCAGTAGGTAAA CGTTGCGGATTATTTCGACG 1539 0.333 52.0
rpoB-rps20_p4 rpoB-rps20 ATAAGCGGCTCTCAGTAGGT GCAGCGCTACTAAAAACTGC 934 0.333 51.8
rpoB-rps20_p5 rpoB-rps20 AGCGGCTCTCAGTAGGTAAA GCAGCGCTACTAAAAACTGC 931 0.333 51.2
petA-chlI_p1 petA-chlI GGTGGCTTTGGTCAAGAAGA GCAAAAGCACATGCAGCATA 1005 0.333 53.2
petA-chlI_p2 petA-chlI GTAATCGTGGTCGTGGTCAA GCAAAAGCACATGCAGCATA 1247 0.333 52.8
petA-chlI_p3 petA-chlI GGTGGCTTTGGTCAAGAAGA TCCGGCTCGATTTGTATTGG 1345 0.333 52.8
petA-chlI_p4 petA-chlI TTGGTGCTGATGGTAAACCC GCAAAAGCACATGCAGCATA 1523 0.333 52.7
petA-chlI_p5 petA-chlI GTTGTTGCACCTGATCCAGA GCAAAAGCACATGCAGCATA 1314 0.333 52.5
ftsH-trnT-UGU_p1 ftsH-trnT-UGU CTTGTACGATGGCATTCCGA AACCCCCAACCTACGGATTA 551–556 0.667 74.8
ftsH-trnT-UGU_p2 ftsH-trnT-UGU CTTGTACGATGGCATTCCGA CGACCTTGGGCTTATGAGTC 1065–1163 0.667 74.1
ftsH-trnT-UGU_p3 ftsH-trnT-UGU CTGGGCTAGAAGCTTGTACG AACCCCCAACCTACGGATTA 568 0.333 52.5
ftsH-trnT-UGU_p4 ftsH-trnT-UGU CTGGGCTAGAAGCTTGTACG CGACCTTGGGCTTATGAGTC 1077 0.333 52.3
ftsH-trnT-UGU_p5 ftsH-trnT-UGU GGAGATTGACCTGAACCACC AACCCCCAACCTACGGATTA 797 0.333 52.2
trnS-GCU-trnD-GUC_p1 trnS-GCU-trnD-GUC AATGGCTGAGTGGTCGAAAG AGACTCGAACTCGCAACTTC 216–218 1.000 85.1
trnS-GCU-trnD-GUC_p2 trnS-GCU-trnD-GUC AATGGCTGAGTGGTCGAAAG GAGACTCGAACTCGCAACTT 217–219 1.000 85.1
trnS-GCU-trnD-GUC_p3 trnS-GCU-trnD-GUC GAAATGGCTGAGTGGTCGAA AGACTCGAACTCGCAACTTC 218–220 1.000 85.0
trnS-GCU-trnD-GUC_p4 trnS-GCU-trnD-GUC GAAATGGCTGAGTGGTCGAA GAGACTCGAACTCGCAACTT 219–221 1.000 85.0
trnS-GCU-trnD-GUC_p5 trnS-GCU-trnD-GUC GGAGAAATGGCTGAGTGGTC AGACTCGAACTCGCAACTTC 221–223 1.000 84.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Discostella asterocostata PV423711.1 129144 View on NCBI ↗
Discostella stelligera PV423714.1 128523 View on NCBI ↗
Discostella stelligeroides PV423672.1 128296 View on NCBI ↗